RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
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`run-simplify.sh` fails if there is no major/minor release specified #338

Open ecwood opened 11 months ago

ecwood commented 11 months ago

This is a symptom of #216

+ echo '================= starting run-simplify.sh =================='
================= starting run-simplify.sh ==================
+ date
Sun Jul 30 17:50:00 UTC 2023
++ dirname /home/ubuntu/kg2-code/run-simplify.sh
+ CONFIG_DIR=/home/ubuntu/kg2-code
+ source /home/ubuntu/kg2-code/master-config.shinc
++ '[' -z ']'
++ test_suffix=
++ BUILD_DIR=/home/ubuntu/kg2-build
++ VENV_DIR=/home/ubuntu/kg2-venv
++ CODE_DIR=/home/ubuntu/kg2-code
++ umls_dir=/home/ubuntu/kg2-build/umls
++ umls_dest_dir=/home/ubuntu/kg2-build/umls/META
++ s3_region=us-west-2
++ s3_bucket=rtx-kg2
++ s3_bucket_public=rtx-kg2-public
++ s3_bucket_versioned=rtx-kg2-versioned
++ s3_cp_cmd='aws s3 cp --no-progress --region us-west-2'
++ mysql_conf=/home/ubuntu/kg2-build/mysql-config.conf
++ curl_get='curl -s -L -f -k'
++ python_command='/home/ubuntu/kg2-venv/bin/python3 -u'
++ curies_to_categories_file=/home/ubuntu/kg2-code/curies-to-categories.yaml
++ curies_to_urls_file=/home/ubuntu/kg2-code/curies-to-urls-map.yaml
++ predicate_mapping_file=/home/ubuntu/kg2-code/predicate-remap.yaml
++ infores_mapping_file=/home/ubuntu/kg2-code/kg2-provided-by-curie-to-infores-curie.yaml
++ ont_load_inventory_file=/home/ubuntu/kg2-code/ont-load-inventory.yaml
++ umls2rdf_config_master=/home/ubuntu/kg2-code/umls2rdf-umls.conf
++ rtx_config_file=RTXConfiguration-config.json
++ biolink_model_version=3.5.2
+ trigger_file_is_major_release=/home/ubuntu/kg2-build/major-release
+ trigger_file_is_minor_release=/home/ubuntu/kg2-build/minor-release
+ input_nodes_json=/home/ubuntu/kg2-build/kg2-merged-nodes.jsonl
+ input_edges_json=/home/ubuntu/kg2-build/kg2-merged-edges.jsonl
+ output_nodes_json=/home/ubuntu/kg2-build/kg2-simplified-nodes.jsonl
+ output_edges_json=/home/ubuntu/kg2-build/kg2-simplified-edges.jsonl
+ local_version_filename=/home/ubuntu/kg2-build/kg2-version.txt
+ build_flag=
+ s3_version_filename=kg2-version.txt
+ aws s3 cp --no-progress --region us-west-2 s3://rtx-kg2-public/kg2-version.txt /home/ubuntu/kg2-build/kg2-version.txt
download: s3://rtx-kg2-public/kg2-version.txt to kg2-build/kg2-version.txt
+ test_flag=
+ [[ '' == \t\e\s\t ]]
+ '[' -e /home/ubuntu/kg2-build/major-release ']'
+ '[' -e /home/ubuntu/kg2-build/minor-release ']'
/home/ubuntu/kg2-code/run-simplify.sh: line 50: increment_flag: unbound variable